2LTQ

High resolution structure of DsbB C41S by joint calculation with solid-state NMR and X-ray data


Experimental Data Snapshot

  • Method: SOLID-STATE NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Structure of the Disulfide Bond Generating Membrane Protein DsbB in the Lipid Bilayer.

Tang, M.Nesbitt, A.E.Sperling, L.J.Berthold, D.A.Schwieters, C.D.Gennis, R.B.Rienstra, C.M.

(2013) J Mol Biol 425: 1670-1682

  • DOI: https://doi.org/10.1016/j.jmb.2013.02.009
  • Primary Citation of Related Structures:  
    2LTQ

  • PubMed Abstract: 

    The integral membrane protein DsbB in Escherichia coli is responsible for oxidizing the periplasmic protein DsbA, which forms disulfide bonds in substrate proteins. We have developed a high-resolution structural model by combining experimental X-ray and solid-state NMR with molecular dynamics (MD) simulations. We embedded the high-resolution DsbB structure, derived from the joint calculation with X-ray reflections and solid-state NMR restraints, into the lipid bilayer and performed MD simulations to provide a mechanistic view of DsbB function in the membrane. Further, we revealed the membrane topology of DsbB by selective proton spin diffusion experiments, which directly probe the correlations of DsbB with water and lipid acyl chains. NMR data also support the model of a flexible periplasmic loop and an interhelical hydrogen bond between Glu26 and Tyr153.


  • Organizational Affiliation

    Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Disulfide bond formation protein B
A, D
176Escherichia coli K-12Mutation(s): 3 
Gene Names: dsbBroxBycgAb1185JW5182
Membrane Entity: Yes 
UniProt
Find proteins for P0A6M2 (Escherichia coli (strain K12))
Explore P0A6M2 
Go to UniProtKB:  P0A6M2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A6M2
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Fab fragment light chain
B, E
239Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Fab fragment heavy chain
C, F
221Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
UQ8
Query on UQ8

Download Ideal Coordinates CCD File 
G [auth A],
H [auth D]
Ubiquinone-8
C49 H74 O4
ICFIZJQGJAJRSU-SGHXUWJISA-N
Experimental Data & Validation

Experimental Data

  • Method: SOLID-STATE NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-02-27
    Type: Initial release
  • Version 1.1: 2013-05-22
    Changes: Database references
  • Version 2.0: 2023-06-14
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Other, Source and taxonomy, Structure summary